Hi biostars,
Is someone aware of how to bulk-download annotation data from ecocyc (biocyc)? For example, I'd like to download an annotation file containing everything in this web-tool; https://www.ecocyc.org/genbro/genbro.shtml?orgid=ECOLI&replicon=COLI-K12
Thanks!
Looks like they offer some data for download. Check SmartTables for E.coli data: https://ecocyc.org/groups?tab=PUBLIC&orgid=ECOLI
Also looks like you may need to get a license even for the EcoCyc.
access to the EcoCyc data files is free, although a license is required
There is a warning in their license doc.
Crawling or scraping the Licensed Materials in any form, for any purpose without SRI's prior written consent is expressly prohibited.
Thank you for directing me to these tables, I'm eligible for an academic license and requested one. I'm surprised that there isn't just some 'master' gff that has everything in a neatly formatted heirarchical format, given the amount of work that went into preparing the webpage....
Do you see a table that would have a list of operons, starts/stops/strands, and the genes they cover in the public data? This is what I really need and am unable to find.
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